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Summary of Progress During the last 12 Months in the Standards Community Model Sharing Working Group Peter Hunter and Herbert M Sauro IMAG Meeting 2012

Summary of Progress During the last 12 Months in the Standards Community

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Summary of Progress During the last 12 Months in the Standards Community. Model Sharing Working Group Peter Hunter and Herbert M Sauro IMAG Meeting 2012. Standards for models, data & software. Experimental measurements. Minimum information standards: MIAME, MICEE,. - PowerPoint PPT Presentation

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Page 1: Summary of  Progress During  the last  12  Months   in  the  Standards Community

Summary of Progress During the last 12 Months in the Standards Community

Model Sharing Working GroupPeter Hunter and Herbert M Sauro

IMAG Meeting 2012

Page 2: Summary of  Progress During  the last  12  Months   in  the  Standards Community

Verification, Benchmarks

Experimental measurements

Model standards: SBML, CellML, FieldML

Model repositories: Biomodels, PMR2

Data standards: DICOM, BioSignalML, ..

Minimum information standards: MIAME, MICEE, ..

Data repositories: PhysioNet, CAPdb, CVRG, ..

Standards for models, data & software

Validation,Limitations

(Journal review)

APIs, webservices

Software: OpenCOR, OpenCMISS, Continuity, Chaste, ..

Simulation standards: SED-MLFunctional curation

APIs, webservices

CurationAnnotation

Referencedescription

Metadata:Ontologies

Need modules!

Metadata:OntologiesGO, FMA, ..

Page 3: Summary of  Progress During  the last  12  Months   in  the  Standards Community

Progress in the SBML Standards World• The Composition/Modularity is now finalized and is supported by

iBioSim (Myers) and Antimony (Lucian, Hucka, Sauro). This allows biochemical models to be modularized.

• The Path2Models consortium project produced over 142,000 qualitative models translated from the KEGG Pathway database, using the draft SBML Level (http://code.google.com/p/path2models/)

• The Level 3 Qualitative Models package specification is almost to the release candidate stage, and is supported in JSBML and libSBML as well as at least 3 other software systems (Boolean networks, logical models and some petri-nets).

• The Level 3 Flux Balance Constraints package definition has stabilized and the authors and considerable progress has been made on the specification document. It's supported in libSBML and will be in the upcoming JSBML 1.0.

• The Level 3 Distribution & Ranges package definition has had a lot of activity surrounding it, as it is an essential part of the European DDmore project.

• Level 3 package documentation pages have be revamped• The SBML Test Suite has been updated with a lot more models (1123

now), especially to test Level 3, as well as enhance and reorganize the model metadata, and updated the online test system at sbml.org.

• There has also been discussion on using SBML to support the exchange of PK/PD Models (See poster by James Sluka for more information).

• New version of libSBML released 5.6• Etc….

DDmore: Drug Disease Model Resources